LAMMPS (12 Jun 2025 - Development - patch_12Jun2025-739-g2644e7f6fa-modified)
  using 1 OpenMP thread(s) per MPI task
units           real
atom_style      full

read_data       data.spce
Reading data file ...
  orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  4500 atoms
  scanning bonds ...
  2 = max bonds/atom
  scanning angles ...
  1 = max angles/atom
  orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736)
  1 by 1 by 1 MPI processor grid
  reading bonds ...
  3000 bonds
  reading angles ...
  1500 angles
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        0        0       
  special bond factors coul:  0        0        0       
     2 = max # of 1-2 neighbors
     1 = max # of 1-3 neighbors
     1 = max # of 1-4 neighbors
     2 = max # of special neighbors
  special bonds CPU = 0.001 seconds
  read_data CPU = 0.026 seconds

pair_style      python 12.0
pair_coeff      * * py_pot.LJCutSPCE OW HW

bond_style      harmonic
angle_style     harmonic
dihedral_style  none
improper_style  none

bond_coeff      1 1000.00 1.000
angle_coeff     1 100.0 109.47

special_bonds   lj/coul 0.0 0.0 1.0
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        0        1       
  special bond factors coul:  0        0        1       
     2 = max # of 1-2 neighbors
     1 = max # of 1-3 neighbors
     2 = max # of special neighbors
  special bonds CPU = 0.001 seconds

neighbor        2.0 bin

fix             1 all shake 0.0001 20 0 b 1 a 1
Finding SHAKE clusters ...
       0 = # of size 2 clusters
       0 = # of size 3 clusters
       0 = # of size 4 clusters
    1500 = # of frozen angles
  find clusters CPU = 0.001 seconds
fix             2 all nvt temp 300.0 300.0 100.0

# create only lj/cut table for the oxygen atoms from python
shell rm -f spce.table
pair_write      1 1 2000 rsq 0.1 12 spce.table OW-OW
Creating table file spce.table with DATE: 2025-07-14
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 14
  ghost atom cutoff = 14
  binsize = 7, bins = 6 6 6
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair python, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d
      bin: standard

# switch to tabulated potential with long-range coulomb as overlay
pair_style      hybrid/overlay coul/long 12.0 table linear 2000
kspace_style    pppm 1.0e-6
pair_coeff      * * coul/long
pair_coeff      1 1 table spce.table OW-OW
Reading pair table potential file spce.table with DATE: 2025-07-14
WARNING: 1 of 2000 force values in table OW-OW are inconsistent with -dE/dr.
WARNING:  Should only be flagged at inflection points (src/pair_table.cpp:469)

thermo 10
run 100
PPPM initialization ...
  using 12-bit tables for long-range coulomb
  G vector (1/distance) = 0.27965195
  grid = 40 40 40
  stencil order = 5
  estimated absolute RMS force accuracy = 0.000394674
  estimated relative force accuracy = 1.188549e-06
  using double precision FFTW3
  3d grid and FFT values/proc = 103823 64000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 14
  ghost atom cutoff = 14
  binsize = 7, bins = 6 6 6
  2 neighbor lists, perpetual/occasional/extra = 2 0 0
  (1) pair coul/long, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d
      bin: standard
  (2) pair table, perpetual, skip from (1)
      attributes: half, newton on
      pair build: skip
      stencil: none
      bin: none
Per MPI rank memory allocation (min/avg/max) = 37.03 | 37.03 | 37.03 Mbytes
   Step          Temp          E_pair         E_mol          TotEng         Press     
         0   0             -16690.019      0             -16690.019     -1268.9123    
        10   120.58553     -17767.489      0             -16689.521     -4063.8134    
        20   136.11736     -17882.538      0             -16665.724     -5124.6191    
        30   137.00764     -17872.301      0             -16647.528     -5337.1509    
        40   153.38867     -17999.256      0             -16628.046     -5213.5617    
        50   167.70342     -18103.046      0             -16603.87      -4460.622     
        60   163.07134     -18034.842      0             -16577.074     -3284.9619    
        70   169.59286     -18064.622      0             -16548.555     -2606.3637    
        80   182.92892     -18153.485      0             -16518.202     -2385.4748    
        90   191.27929     -18195.343      0             -16485.411     -2235.3292    
       100   194.68586     -18192.445      0             -16452.061     -1948.3379    
Loop time of 2.57844 on 1 procs for 100 steps with 4500 atoms

Performance: 3.351 ns/day, 7.162 hours/ns, 38.783 timesteps/s, 174.524 katom-step/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 2.0568     | 2.0568     | 2.0568     |   0.0 | 79.77
Bond    | 7.4804e-05 | 7.4804e-05 | 7.4804e-05 |   0.0 |  0.00
Kspace  | 0.39621    | 0.39621    | 0.39621    |   0.0 | 15.37
Neigh   | 0.092514   | 0.092514   | 0.092514   |   0.0 |  3.59
Comm    | 0.0068884  | 0.0068884  | 0.0068884  |   0.0 |  0.27
Output  | 0.00032237 | 0.00032237 | 0.00032237 |   0.0 |  0.01
Modify  | 0.023601   | 0.023601   | 0.023601   |   0.0 |  0.92
Other   |            | 0.002014   |            |       |  0.08

Nlocal:           4500 ave        4500 max        4500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:          21216 ave       21216 max       21216 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    2.60177e+06 ave 2.60177e+06 max 2.60177e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 2601768
Ave neighs/atom = 578.17067
Ave special neighs/atom = 2
Neighbor list builds = 3
Dangerous builds = 0

shell rm spce.table

Total wall time: 0:00:02
